├── tests
├── __init__.py
├── test_files
│ ├── .gitignore
│ ├── label_map.txt
│ ├── page1.jpg
│ ├── alto_dataset
│ │ ├── output.jpg
│ │ ├── Bruyere07.jpg
│ │ ├── Bruyere09.jpg
│ │ ├── Bruyere07.xml
│ │ └── Bruyere09.xml
│ ├── annot2.txt
│ └── annot1.txt
├── nano-yolo-ladas.pt
├── test_utils.py
├── test_convert.py
└── test_kraken.py
├── yaltai
├── __init__.py
├── cli
│ ├── __init__.py
│ ├── krakn.py
│ └── yaltai.py
├── models
│ ├── __init__.py
│ ├── yolo.py
│ └── krakn.py
├── template.xml
├── preprocessing.py
└── utils.py
├── MANIFEST.in
├── requirements.txt
├── .github
└── workflows
│ └── test.yml
├── CITATION.CFF
├── README.md
├── .gitignore
├── setup.py
└── LICENSE
/tests/__init__.py:
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1 |
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/yaltai/__init__.py:
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1 |
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/yaltai/cli/__init__.py:
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1 |
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/yaltai/models/__init__.py:
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1 |
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/MANIFEST.in:
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1 | include yaltai/template.xml
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/tests/test_files/.gitignore:
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1 | page1.xml
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/tests/test_files/label_map.txt:
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1 | Class0
2 | Class1
3 |
4 | Stuff
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/tests/nano-yolo-ladas.pt:
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https://raw.githubusercontent.com/PonteIneptique/YALTAi/HEAD/tests/nano-yolo-ladas.pt
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/tests/test_files/page1.jpg:
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https://raw.githubusercontent.com/PonteIneptique/YALTAi/HEAD/tests/test_files/page1.jpg
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/requirements.txt:
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1 | kraken~=5.3.0
2 | mean-average-precision==2021.4.26.0
3 | tabulate~=0.8.10
4 | ultralytics~=8.3.0
5 | fast_deskew==1.0
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/tests/test_files/alto_dataset/output.jpg:
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https://raw.githubusercontent.com/PonteIneptique/YALTAi/HEAD/tests/test_files/alto_dataset/output.jpg
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/tests/test_files/alto_dataset/Bruyere07.jpg:
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https://raw.githubusercontent.com/PonteIneptique/YALTAi/HEAD/tests/test_files/alto_dataset/Bruyere07.jpg
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/tests/test_files/alto_dataset/Bruyere09.jpg:
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https://raw.githubusercontent.com/PonteIneptique/YALTAi/HEAD/tests/test_files/alto_dataset/Bruyere09.jpg
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/tests/test_files/annot2.txt:
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1 | 23 0.4914115952466691 0.45760844079718643 0.6449045732805185 0.4102297772567409
2 | 23 0.4933705437522506 0.7764806565064478 0.6465250270075622 0.2320398593200469
3 | 31 0.7885343896290963 0.11840562719812427 0.033172488296723084 0.026182883939038688
4 | 35 0.4834569679510263 0.1191535756154748 0.4334101548433561 0.024438452520515828
5 | 24 0.48678790061217136 0.20451113716295427 0.6372740367302845 0.10247831184056272
6 | 28 0.47840835433921497 0.14436342321219228 0.24528628015844436 0.025828839390386868
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/tests/test_files/annot1.txt:
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1 | 14 0.49139869729173813 0.3715823573386494 0.6673020226259856 0.07884874158983304
2 | 14 0.49408639012684263 0.23613506105158236 0.6722831676379842 0.15367804634936458
3 | 35 0.49086047308878983 0.1285771243458759 0.26186150154268084 0.03464490406179915
4 | 31 0.8086732944806309 0.13971592324943932 0.03529310935893041 0.03310740094692251
5 | 14 0.49913952691121016 0.594151507600299 0.6766986630099417 0.31005232992773485
6 | 14 0.507857387727117 0.8290804884126588 0.6902228316763799 0.1168950909543982
7 | 1 0.9231984916009598 0.4728781460254174 0.1535995886184436 0.18793919760777475
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/yaltai/template.xml:
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1 |
2 |
5 |
6 | pixel
7 |
8 | %Filename%
9 |
10 |
11 |
12 |
13 |
14 | %Tags%
15 |
16 |
17 |
18 |
21 |
25 | %Textblocks%
26 |
27 |
28 |
29 |
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/.github/workflows/test.yml:
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1 | # This workflow will install Python dependencies, run tests and lint with a single version of Python
2 | # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
3 |
4 | name: Test
5 |
6 | on: [push, pull_request]
7 |
8 | jobs:
9 | test:
10 | runs-on: ubuntu-latest
11 | strategy:
12 | matrix:
13 | python-version: ["3.8", "3.9", "3.10", "3.11"]
14 | steps:
15 | - uses: actions/checkout@v4
16 | - name: Set up Python
17 | uses: actions/setup-python@v5
18 | with:
19 | python-version: ${{ matrix.python-version }}
20 | - name: Display Python version
21 | run: python -c "import sys; print(sys.version)"
22 | - name: Install dependencies
23 | run: |
24 | pip install -r requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu
25 | pip install pytest pytest-cov coveralls pytest-sugar
26 | - name: Run Tests
27 | run: |
28 | pytest --doctest-modules --cov=yaltai --verbose
29 |
--------------------------------------------------------------------------------
/CITATION.CFF:
--------------------------------------------------------------------------------
1 | # This CITATION.cff file was generated with cffinit.
2 | # Visit https://bit.ly/cffinit to generate yours today!
3 |
4 | cff-version: 1.2.0
5 | title: 'YALTAi: You Actually Look Twice At it'
6 | message: "If you use this software, please cite both the article from preferred-citation and the software itself."
7 | type: software
8 | authors:
9 | - given-names: Thibault
10 | family-names: Clérice
11 | email: thibault.clerice@inria.fr
12 | affiliation: Inria
13 | orcid: 'https://orcid.org/0000-0003-1852-9204'
14 | identifiers:
15 | - type: swh
16 | value: 'swh:1:snp:d9ca209ae2271537ff57d3748c8a76c49fd6222b'
17 | - type: other
18 | value: 'https://enc.hal.science/hal-03723208v3'
19 | description: Paper
20 | repository-code: 'https://github.com/PonteIneptique/yaltai'
21 | url: 'https://pypi.org/project/YALTAi/'
22 | license: GPL-3.0
23 | version: 1.0.0
24 | date-released: '2023-01-01'
25 | preferred-citation:
26 | authors:
27 | - family-names: Clérice
28 | given-names: Thibault
29 | title: "You Actually Look Twice At it (YALTAi): using an object detection approach instead of region segmentation within the Kraken engine"
30 | type: article
31 | volume-title: 'Historical Documents and automatic text recognition'
32 | journal: "Journal of Data Mining & Digital Humanities"
33 | doi: 'doi.org/10.46298/jdmdh.9806'
34 | date-published: "2023-12-01"
35 |
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/yaltai/preprocessing.py:
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1 | from typing import Tuple, List
2 | from PIL import Image
3 | import fast_deskew
4 | import cv2
5 | import numpy as np
6 |
7 |
8 | def deskew(image: str) -> Tuple[Image.Image, float]:
9 | _, best_angle = fast_deskew.deskew_image(image, False)
10 | img = Image.open(image)
11 | return img.rotate(best_angle), best_angle
12 |
13 |
14 | def rotatebox(bbox: List[List[int]], image: Image.Image, angle: float):
15 | # https://gist.githubusercontent.com/Joanne03/5941a9b4db4fa7c652a2d7f67b11a09b/raw/f99b2f18ad0fbe680ac631e531782b957f158def/rotate_bbox.py
16 | height, width = image.size
17 | image_center_x, image_center_y = width // 2, height // 2
18 |
19 | rotated_bbox = []
20 |
21 | for i, coord in enumerate(bbox):
22 | rot_matrix = cv2.getRotationMatrix2D((image_center_x, image_center_y), angle, 1.0)
23 | cosinus, sinus = abs(rot_matrix[0, 0]), abs(rot_matrix[0, 1])
24 | new_width = int((height * sinus) + (width * cosinus))
25 | new_height = int((height * cosinus) + (width * sinus))
26 | rot_matrix[0, 2] += (new_width / 2) - image_center_x
27 | rot_matrix[1, 2] += (new_height / 2) - image_center_y
28 | v = [coord[0], coord[1], 1] # ?
29 | adjusted_coord = np.dot(rot_matrix, v)
30 | rotated_bbox.append((int(adjusted_coord[0]), int(adjusted_coord[1])))
31 |
32 | return rotated_bbox
33 |
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/yaltai/models/yolo.py:
--------------------------------------------------------------------------------
1 | from typing import List, Dict
2 | from ultralytics import YOLO
3 | from ultralytics.engine.results import Results
4 |
5 | from yaltai.preprocessing import deskew, rotatebox
6 |
7 |
8 | def segment(
9 | model: YOLO,
10 | input: str,
11 | apply_deskew: bool = False,
12 | max_angle: float = 10.0
13 | ) -> Dict[str, List[List[int]]]:
14 | """
15 |
16 | Returns {
17 | cls_name: [
18 | [[x0, y0], [x1, y0], [x1, y1], [x0, y1], [x0, y0]]
19 | ]
20 | }
21 | """
22 | rotated_input = None
23 | angle = 0
24 | predictions: List[Results] = []
25 | if apply_deskew:
26 | rotated_input, angle = deskew(input)
27 | if abs(angle) > max_angle:
28 | predictions = model.predict(input, save=False)
29 | rotated_input = None
30 | else:
31 | predictions = model.predict(rotated_input, save=False)
32 | else:
33 | predictions = model.predict(input, save=False)
34 |
35 | names: List[str] = list(set([
36 | name
37 | for res in predictions
38 | for name in res.names.values()
39 | ]))
40 |
41 | out = {
42 | name: []
43 | for name in names
44 | }
45 | for pred in predictions:
46 | for box, cls_id in zip(pred.boxes.xyxy, pred.boxes.cls):
47 | cls_name = pred.names[cls_id.item()]
48 | x0, y0, x1, y1 = box.tolist()
49 | points = [[x0, y0], [x1, y0], [x1, y1], [x0, y1], [x0, y0]]
50 |
51 | if apply_deskew and rotated_input is not None:
52 | points = rotatebox(points, rotated_input, -angle)
53 | points.append(points[0])
54 | out[cls_name].append(points)
55 |
56 | return out
57 |
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/README.md:
--------------------------------------------------------------------------------
1 | # YALTAi
2 | You Actually Look Twice At it
3 |
4 | This provides an adapter for Kraken to use YOLOv8 (1.0.0 update; use previous version to reuse YOLOv5 models) Object Detection routine.
5 |
6 | This tool can be used for both segmenting and conversion of models.
7 |
8 | # Routine
9 |
10 | ## Instal
11 |
12 | ```bash
13 | pip install YALTAi
14 | ```
15 |
16 | ## Training
17 |
18 | Convert (and split optionally) your data
19 |
20 | ```bash
21 | # Keeps .1 data in the validation set and convert all alto into YOLOv5 format
22 | # Keeps the segmonto information up to the regions
23 | yaltai convert alto-to-yolo PATH/TO/ALTOorPAGE/*.xml my-dataset --shuffle .1 --segmonto region
24 | ```
25 |
26 | And then [train YOLO](https://github.com/ultralytics/yolov5/wiki/Train-Custom-Data)
27 |
28 | ```bash
29 | yolo task=detect mode=train model=yolov8n.pt data=my-dataset/config.yml epochs=100 plots=True device=0 batch=8 imgsz=960
30 | ```
31 |
32 | ## Predicting
33 |
34 | YALTAi has the same CLI interface as Kraken, so:
35 |
36 | - You can use base BLLA model for line or provide yours with `-i model.mlmodel`
37 | - Use a GPU (`--device cuda:0`) or a CPU (`--device cpu`)
38 | - Apply on batch (`*.jpg`)
39 |
40 | ```bash
41 | # Retrieve the best.pt after the training
42 | # It should be in runs/train/exp[NUMBER]/weights/best.pt
43 | # And then annotate your new data with the same CLI API as Kraken !
44 | yaltai kraken --device cuda:0 -I "*.jpg" --suffix ".xml" segment --yolo runs/train/exp5/weights/best.pt
45 | ```
46 |
47 | ## Metrics
48 |
49 | The metrics produced from various libraries never gives the same mAP or Precision. I tried
50 |
51 | - `object-detection-metrics==0.4`
52 | - `mapCalc`
53 | - `mean-average-precision` which ended up being the chosen one (cleanest in terms of how I can access info)
54 |
55 | and of course I compared with YOLOv5 raw results. Nothing worked the same. And the library YOLOv5 derives its metrics from is uninstallable through pip.
56 |
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/tests/test_utils.py:
--------------------------------------------------------------------------------
1 | import os
2 | import numpy as np
3 | from yaltai.utils import read_labelmap, parse_box_labels, XYXY
4 |
5 |
6 | def test_read_labelmap():
7 | """Asserts that reading a label map works"""
8 | labels = read_labelmap(os.path.join(
9 | os.path.dirname(__file__),
10 | "test_files",
11 | "label_map.txt"
12 | ))
13 | assert labels == ["Class0", "Class1", "Stuff"]
14 |
15 |
16 | def test_read_files():
17 | """Asserts that parsing COCO/YOLO formats work"""
18 | annots, arrays = parse_box_labels([
19 | os.path.join(
20 | os.path.dirname(__file__),
21 | "test_files",
22 | "annot1.txt"
23 | ),
24 | os.path.join(
25 | os.path.dirname(__file__),
26 | "test_files",
27 | "annot2.txt"
28 | )
29 | ])
30 | assert annots == {
31 | 'boxes': [
32 | XYXY(x0=15, y0=33, x1=82, y1=41),
33 | XYXY(x0=15, y0=15, x1=83, y1=31),
34 | XYXY(x0=35, y0=11, x1=62, y1=14),
35 | XYXY(x0=79, y0=12, x1=82, y1=15),
36 | XYXY(x0=16, y0=43, x1=83, y1=74),
37 | XYXY(x0=16, y0=77, x1=85, y1=88),
38 | XYXY(x0=84, y0=37, x1=99, y1=56),
39 | XYXY(x0=16, y0=25, x1=81, y1=66),
40 | XYXY(x0=17, y0=66, x1=81, y1=89),
41 | XYXY(x0=77, y0=10, x1=80, y1=13),
42 | XYXY(x0=26, y0=10, x1=70, y1=13),
43 | XYXY(x0=16, y0=15, x1=80, y1=25),
44 | XYXY(x0=35, y0=13, x1=60, y1=15)
45 | ],
46 | 'labels': [14, 14, 35, 31, 14, 14, 1, 23, 23, 31, 35, 24, 28]
47 | }
48 | assert (arrays[0] == np.array([[15, 33, 82, 41, 14, 0, 0],
49 | [15, 15, 83, 31, 14, 0, 0],
50 | [35, 11, 62, 14, 35, 0, 0],
51 | [79, 12, 82, 15, 31, 0, 0],
52 | [16, 43, 83, 74, 14, 0, 0],
53 | [16, 77, 85, 88, 14, 0, 0],
54 | [84, 37, 99, 56, 1, 0, 0]])).all()
55 | assert (arrays[1] == np.array([[16, 25, 81, 66, 23, 0, 0],
56 | [17, 66, 81, 89, 23, 0, 0],
57 | [77, 10, 80, 13, 31, 0, 0],
58 | [26, 10, 70, 13, 35, 0, 0],
59 | [16, 15, 80, 25, 24, 0, 0],
60 | [35, 13, 60, 15, 28, 0, 0]])).all()
61 |
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/tests/test_convert.py:
--------------------------------------------------------------------------------
1 | import tempfile
2 | import os
3 | import glob
4 | from click.testing import CliRunner
5 |
6 | from yaltai.cli.yaltai import yaltai_cli
7 |
8 |
9 | def test_yaltai_single_alto_to_xml():
10 | """Ensures that we can convert to YOLO format"""
11 | runner = CliRunner()
12 |
13 | with tempfile.TemporaryDirectory() as tempdir:
14 | # Run the Click command
15 | result = runner.invoke(
16 | yaltai_cli,
17 | [
18 | "convert",
19 | "alto-to-yolo",
20 | os.path.join(os.path.abspath(os.path.dirname(__file__)), "test_files", "alto_dataset", "output.xml"),
21 | tempdir,
22 | ])
23 |
24 | # Ensure the command ran successfully
25 | assert result.exit_code == 0
26 | assert "Found 1 to convert." in result.output
27 | assert "- 00001 NumberingZone" in result.output, "Correct number of zone types are found"
28 | assert "- 00001 RunningTitleZone" in result.output, "Correct number of zone types are found"
29 | assert "- 00001 MainZone-P-Continued" in result.output, "Correct number of zone types are found"
30 | assert "- 00004 MainZone-P" in result.output, "Correct number of zone types are found"
31 | with open(os.path.join(tempdir, "labels", "output.txt")) as f:
32 | data = [line.split() for line in f.read().split("\n")]
33 | assert data == [
34 | ['0', '0.345606', '0.117500', '0.037501', '0.020206'],
35 | ['1', '0.612827', '0.118333', '0.212882', '0.020736'],
36 | ['2', '0.616390', '0.210833', '0.578172', '0.142851'],
37 | ['3', '0.616390', '0.365833', '0.577029', '0.162800'],
38 | ['3', '0.616390', '0.547500', '0.574365', '0.199581'],
39 | ['3', '0.616390', '0.727500', '0.576050', '0.161861'],
40 | ['3', '0.611639', '0.819167', '0.583077', '0.022773']
41 | ]
42 |
43 |
44 | def test_yaltai_shuffle_alto_to_xml():
45 | """Ensures that we can convert to YOLO format"""
46 | runner = CliRunner()
47 |
48 | with tempfile.TemporaryDirectory() as tempdir:
49 | # Run the Click command
50 | result = runner.invoke(
51 | yaltai_cli,
52 | [
53 | "convert",
54 | "alto-to-yolo",
55 | "--shuffle",
56 | ".3",
57 | *glob.glob(os.path.join(os.path.abspath(os.path.dirname(__file__)), "test_files", "alto_dataset", "*.xml")),
58 | tempdir,
59 | ])
60 | assert "Found 3 to convert." in result.output
61 | assert "1/3 image for validation." in result.output
62 | assert result.exit_code == 0
63 |
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/.gitignore:
--------------------------------------------------------------------------------
1 | # Yolo data for test
2 | nl
3 | *.pt
4 | *.mlmodel
5 | # Test results
6 | test_*.jpg
7 | test_*.xml
8 | converted
9 | my-dataset
10 | ex
11 | table-test
12 | runs
13 | yolo-dataset
14 | *.tar.gz
15 | *.sh
16 | # PyCharm
17 | .idea
18 | # Byte-compiled / optimized / DLL files
19 | __pycache__/
20 | *.py[cod]
21 | *$py.class
22 |
23 | # C extensions
24 | *.so
25 |
26 | # Distribution / packaging
27 | .Python
28 | build/
29 | develop-eggs/
30 | dist/
31 | downloads/
32 | eggs/
33 | .eggs/
34 | lib/
35 | lib64/
36 | parts/
37 | sdist/
38 | var/
39 | wheels/
40 | pip-wheel-metadata/
41 | share/python-wheels/
42 | *.egg-info/
43 | .installed.cfg
44 | *.egg
45 | MANIFEST
46 |
47 | # PyInstaller
48 | # Usually these files are written by a python script from a template
49 | # before PyInstaller builds the exe, so as to inject date/other infos into it.
50 | *.manifest
51 | *.spec
52 |
53 | # Installer logs
54 | pip-log.txt
55 | pip-delete-this-directory.txt
56 |
57 | # Unit test / coverage reports
58 | htmlcov/
59 | .tox/
60 | .nox/
61 | .coverage
62 | .coverage.*
63 | .cache
64 | nosetests.xml
65 | coverage.xml
66 | *.cover
67 | *.py,cover
68 | .hypothesis/
69 | .pytest_cache/
70 |
71 | # Translations
72 | *.mo
73 | *.pot
74 |
75 | # Django stuff:
76 | *.log
77 | local_settings.py
78 | db.sqlite3
79 | db.sqlite3-journal
80 |
81 | # Flask stuff:
82 | instance/
83 | .webassets-cache
84 |
85 | # Scrapy stuff:
86 | .scrapy
87 |
88 | # Sphinx documentation
89 | docs/_build/
90 |
91 | # PyBuilder
92 | target/
93 |
94 | # Jupyter Notebook
95 | .ipynb_checkpoints
96 |
97 | # IPython
98 | profile_default/
99 | ipython_config.py
100 |
101 | # pyenv
102 | .python-version
103 |
104 | # pipenv
105 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
106 | # However, in case of collaboration, if having platform-specific dependencies or dependencies
107 | # having no cross-platform support, pipenv may install dependencies that don't work, or not
108 | # install all needed dependencies.
109 | #Pipfile.lock
110 |
111 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow
112 | __pypackages__/
113 |
114 | # Celery stuff
115 | celerybeat-schedule
116 | celerybeat.pid
117 |
118 | # SageMath parsed files
119 | *.sage.py
120 |
121 | # Environments
122 | .env
123 | .venv
124 | env/
125 | venv/
126 | ENV/
127 | env.bak/
128 | venv.bak/
129 |
130 | # Spyder project settings
131 | .spyderproject
132 | .spyproject
133 |
134 | # Rope project settings
135 | .ropeproject
136 |
137 | # mkdocs documentation
138 | /site
139 |
140 | # mypy
141 | .mypy_cache/
142 | .dmypy.json
143 | dmypy.json
144 |
145 | # Pyre type checker
146 | .pyre/
147 | /article-dataset/
148 |
--------------------------------------------------------------------------------
/yaltai/utils.py:
--------------------------------------------------------------------------------
1 | from dataclasses import dataclass
2 | from collections import namedtuple
3 | from typing import List, Tuple, Optional, Dict, Union
4 | from pathlib import Path
5 | import numpy as np
6 |
7 | XYXY = namedtuple("XYXY", ["x0", "y0", "x1", "y1"])
8 |
9 |
10 | @dataclass
11 | class AltoToYoloZone:
12 | BOX: List[Tuple[int, int]]
13 | PAGE_WIDTH: int
14 | PAGE_HEIGHT: int
15 | tag: int
16 | _xywh: Optional[Tuple[int, int, int, int]] = None
17 |
18 | @property
19 | def height(self):
20 | return self.xywh[-1]
21 |
22 | @property
23 | def width(self):
24 | return self.xywh[-2]
25 |
26 | @property
27 | def x_center(self) -> int:
28 | return int(self.width / 2 + self.xywh[0])
29 |
30 | @property
31 | def y_center(self) -> int:
32 | return int(self.height / 2 + self.xywh[1])
33 |
34 | @property
35 | def xywh(self):
36 | if self._xywh:
37 | return self._xywh
38 |
39 | box = np.array(self.BOX)
40 | x_min, y_min = box.min(axis=0)
41 | x_max, y_max = box.max(axis=0)
42 |
43 | width = x_max - x_min
44 | height = y_max - y_min
45 |
46 | self._xywh = (x_min, y_min, width, height)
47 | return self._xywh
48 |
49 | def yoloV5(self):
50 | try:
51 | return (f"{self.tag}"
52 | f" {self.x_center / self.PAGE_WIDTH:.6f}"
53 | f" {self.y_center / self.PAGE_HEIGHT:.6f}"
54 | f" {self.width / self.PAGE_WIDTH:.6f}"
55 | f" {self.height / self.PAGE_HEIGHT:.6f}")
56 | except Exception as E:
57 | print(E)
58 | return None
59 |
60 |
61 | @dataclass
62 | class YoloV5Zone:
63 | tag: int
64 | xc: float
65 | yc: float
66 | w: float
67 | h: float
68 |
69 | @classmethod
70 | def from_txt(cls, tag, *box):
71 | return YoloV5Zone(int(tag), *[float(b) for b in box])
72 |
73 | @property
74 | def xyxy(self):
75 | return XYXY(
76 | self.xc - self.w / 2,
77 | self.yc - self.h / 2,
78 | self.xc + self.w / 2,
79 | self.yc + self.h / 2
80 | )
81 |
82 | @property
83 | def xyxy100(self):
84 | return XYXY(
85 | *[int(100 * b) for b in self.xyxy]
86 | )
87 |
88 |
89 | def parse_box_labels(
90 | files: List[str],
91 | gt: bool = True
92 | ) -> Tuple[Dict[str, Union[List[Union[XYXY, int]]]], List[np.array]]:
93 | """Parse a list of YOLO/COCO BB annotation files
94 |
95 | This function is only used to compute metrics
96 |
97 | :param files: List of file path in YOLO / COCO formats
98 | :param gt: If data are ground Truth of if they are predicted (I don't remember why)
99 | """
100 | parsed = {"boxes": [], "labels": []}
101 | arrays = []
102 | for file in sorted(files):
103 | with open(file) as f:
104 | start_index = len(parsed["boxes"])
105 | for line in f:
106 | z = YoloV5Zone.from_txt(*line.strip().split()[:5])
107 | parsed["boxes"].append(z.xyxy100)
108 | parsed["labels"].append(z.tag)
109 | arrays.append(
110 | np.array([
111 | [*xyxy, cls_idx] + ([0, 0] if gt else [1])
112 | for xyxy, cls_idx in zip(parsed["boxes"][start_index:], parsed["labels"][start_index:])
113 | ])
114 | )
115 |
116 | return parsed, arrays
117 |
118 |
119 | def read_labelmap(path: str) -> List[str]:
120 | """ Reads a labelmap YAML file and parses the classes
121 | """
122 | with open(path) as f:
123 | lines = [line.strip() for line in f.read().split() if line.strip()]
124 | return lines
125 |
126 |
127 | def read_manifest(manifest: Union[str, Path]) -> List[str]:
128 | """ Reads a manifest (for training purposes ?)
129 | """
130 | with open(manifest, 'r') as f:
131 | out = [x.strip() for x in f.read().splitlines() if x.strip()]
132 | return out
133 |
--------------------------------------------------------------------------------
/setup.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python
2 | # -*- coding: utf-8 -*-
3 |
4 | # Note: To use the 'upload' functionality of this file, you must:
5 | # $ pip install twine
6 |
7 | import io
8 | import os
9 | import sys
10 | from shutil import rmtree
11 |
12 | from setuptools import find_packages, setup, Command
13 |
14 | here = os.path.abspath(os.path.dirname(__file__))
15 |
16 | # Package meta-data.
17 | NAME = 'YALTAi'
18 | DESCRIPTION = "You Actually Look Twice At it, YOLOv5-Kraken adapter for region detection "
19 | URL = 'https://github.com/ponteineptique/yaltai'
20 | AUTHOR = 'Thibault Clérice'
21 | REQUIRES_PYTHON = '>=3.8.0'
22 | VERSION = "2.0.5"
23 |
24 | # What packages are required for this module to be executed?
25 |
26 | with open(os.path.join(here, 'requirements.txt')) as f:
27 | REQUIRED = f.read().splitlines()
28 |
29 | # What packages are optional?
30 | EXTRAS = {}
31 |
32 | # The rest you shouldn't have to touch too much :)
33 | # ------------------------------------------------
34 | # Except, perhaps the License and Trove Classifiers!
35 | # If you do change the License, remember to change the Trove Classifier for that!
36 |
37 |
38 | # Import the README and use it as the long-description.
39 | # Note: this will only work if 'README.md' is present in your MANIFEST.in file!
40 | try:
41 | with io.open(os.path.join(here, 'README.md'), encoding='utf-8') as f:
42 | long_description = '\n' + f.read()
43 | except FileNotFoundError:
44 | long_description = DESCRIPTION
45 |
46 | # Load the package's __version__.py module as a dictionary.
47 | about = {}
48 | if not VERSION:
49 | project_slug = NAME.lower().replace("-", "_").replace(" ", "_")
50 | with open(os.path.join(here, project_slug, '__version__.py')) as f:
51 | exec(f.read(), about)
52 | else:
53 | about['__version__'] = VERSION
54 |
55 |
56 | class UploadCommand(Command):
57 | """Support setup.py upload."""
58 |
59 | description = 'Build and publish the package.'
60 | user_options = []
61 |
62 | @staticmethod
63 | def status(s):
64 | """Prints things in bold."""
65 | print('\033[1m{0}\033[0m'.format(s))
66 |
67 | def initialize_options(self):
68 | pass
69 |
70 | def finalize_options(self):
71 | pass
72 |
73 | def run(self):
74 | try:
75 | self.status('Removing previous builds…')
76 | rmtree(os.path.join(here, 'dist'))
77 | except OSError:
78 | pass
79 |
80 | self.status('Building Source and Wheel (universal) distribution…')
81 | os.system('{0} setup.py sdist bdist_wheel --universal'.format(sys.executable))
82 |
83 | self.status('Uploading the package to PyPI via Twine…')
84 | os.system('twine upload dist/*')
85 |
86 | self.status('Pushing git tags…')
87 | os.system('git tag v{0}'.format(about['__version__']))
88 | os.system('git push --tags')
89 |
90 | sys.exit()
91 |
92 |
93 | # Where the magic happens:
94 | setup(
95 | name=NAME,
96 | version=about['__version__'],
97 | description=DESCRIPTION,
98 | long_description=long_description,
99 | long_description_content_type='text/markdown',
100 | author=AUTHOR,
101 | python_requires=REQUIRES_PYTHON,
102 | url=URL,
103 | packages=find_packages(exclude=('tests', 'env', 'venv',)),
104 | # If your package is a single module, use this instead of 'packages':
105 | # py_modules=['mypackage'],
106 |
107 | entry_points={
108 | 'console_scripts': ['yaltai=yaltai.cli.yaltai:yaltai_cli'],
109 | },
110 | install_requires=REQUIRED,
111 | extras_require=EXTRAS,
112 | include_package_data=True,
113 | license='MIT',
114 | classifiers=[
115 | # Trove classifiers
116 | # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
117 | 'License :: OSI Approved :: MIT License',
118 | 'Programming Language :: Python',
119 | 'Programming Language :: Python :: 3',
120 | 'Programming Language :: Python :: 3.8',
121 | 'Programming Language :: Python :: Implementation :: CPython',
122 | 'Programming Language :: Python :: Implementation :: PyPy',
123 | 'Topic :: Text Processing :: Linguistic'
124 | ],
125 | # $ setup.py publish support.
126 | cmdclass={
127 | 'upload': UploadCommand,
128 | }
129 | )
130 |
--------------------------------------------------------------------------------
/yaltai/cli/krakn.py:
--------------------------------------------------------------------------------
1 | import click
2 | import os
3 | import dataclasses
4 | from typing import cast
5 | from kraken.kraken import (
6 | # Constants
7 | SEGMENTATION_DEFAULT_MODEL,
8 | # CLI Stuff
9 | message, logger, # Logics
10 | get_input_parser, partial
11 | )
12 | from PIL import Image
13 | from kraken.containers import Segmentation
14 | from ultralytics import YOLO
15 |
16 |
17 | def segmenter(model, text_direction, mask, device, yolo_model, ignore_lines, deskew, max_angle, input, output) -> None:
18 | import json
19 | import yaltai.models.krakn
20 | import yaltai.models.yolo
21 |
22 | ctx = click.get_current_context()
23 |
24 | if ctx.meta['first_process']:
25 | if ctx.meta['input_format_type'] != 'image':
26 | input = get_input_parser(ctx.meta['input_format_type'])(input).imagename
27 | ctx.meta['first_process'] = False
28 |
29 | if 'base_image' not in ctx.meta:
30 | ctx.meta['base_image'] = input
31 |
32 | try:
33 | im = Image.open(input)
34 | except IOError as e:
35 | raise click.BadParameter(str(e))
36 |
37 | if mask:
38 | try:
39 | mask = Image.open(mask)
40 | except IOError as e:
41 | raise click.BadParameter(str(e))
42 |
43 | message(f'Segmenting {ctx.meta["orig_file"]}\t', nl=False)
44 | try:
45 | regions = yaltai.models.yolo.segment(
46 | yolo_model, input=input,
47 | apply_deskew=deskew, max_angle=max_angle
48 | )
49 | res: Segmentation = yaltai.models.krakn.segment(
50 | im, text_direction, mask=mask, model=model, device=device,
51 | regions=regions, ignore_lignes=ignore_lines,
52 | raise_on_error=ctx.meta['raise_failed'], autocast=ctx.meta["autocast"]
53 | )
54 | except Exception as E:
55 | if ctx.meta['raise_failed']:
56 | raise
57 | message('\u2717', fg='red')
58 | ctx.exit(1)
59 |
60 | if ctx.meta['last_process'] and ctx.meta['output_mode'] != 'native':
61 | with click.open_file(output, 'w', encoding='utf-8') as fp:
62 | fp = cast('IO[Any]', fp)
63 | logger.info('Serializing as {} into {}'.format(ctx.meta['output_mode'], output))
64 | from kraken import serialization
65 | fp.write(
66 | serialization.serialize(
67 | results=res,
68 | image_size=im.size,
69 | template=ctx.meta['output_template'],
70 | template_source='custom' if ctx.meta['output_mode'] == 'template' else 'native',
71 | processing_steps=ctx.meta['steps']
72 | )
73 | )
74 | else:
75 | with click.open_file(output, 'w') as fp:
76 | fp = cast('IO[Any]', fp)
77 | json.dump(dataclasses.asdict(res), fp)
78 | message('\u2713', fg='green')
79 |
80 |
81 | from kraken.kraken import cli as kcli
82 |
83 |
84 | @kcli.command('segment')
85 | @click.pass_context
86 | @click.option('-i', '--model',
87 | default=None,
88 | show_default=True, type=click.Path(exists=True),
89 | help='Baseline detection model to use')
90 | @click.option('-y', '--yolo',
91 | default=None,
92 | show_default=True, type=click.Path(exists=True),
93 | help='YOLO model to use')
94 | @click.option('-d', '--text-direction', default='horizontal-lr',
95 | show_default=True,
96 | type=click.Choice(['horizontal-lr', 'horizontal-rl',
97 | 'vertical-lr', 'vertical-rl']),
98 | help='Sets principal text direction')
99 | @click.option('-m', '--mask', show_default=True, default=None,
100 | type=click.File(mode='rb', lazy=True), help='Segmentation mask '
101 | 'suppressing page areas for line detection. 0-valued image '
102 | 'regions are ignored for segmentation purposes. Disables column '
103 | 'detection.')
104 | @click.option('-d', '--deskew', show_default=True, default=False, is_flag=True,
105 | help='Prior to applying YOLO model, '
106 | 'deskew the image: this will produced oriented bounding box. The final output'
107 | 'is realigned with the original image.')
108 | @click.option('--max-angle', show_default=True, default=10, type=float,
109 | help='Maximum deskewing angle')
110 | @click.option('-n', '--ignore-lines', show_default=True, default=False, is_flag=True,
111 | help='Does not run line segmentation through Kraken, only Zone from YOLO')
112 | def yaltai_segment(ctx, model, text_direction, mask, yolo, ignore_lines, deskew, max_angle):
113 | """
114 | Segments page images into text lines.
115 | """
116 |
117 | if not model:
118 | model = SEGMENTATION_DEFAULT_MODEL
119 | if not yolo:
120 | raise Exception("No YOLOv8 model given")
121 | ctx.meta['steps'].append({'category': 'processing',
122 | 'description': 'Baseline and region segmentation',
123 | 'settings': {'model': os.path.basename(model),
124 | 'text_direction': text_direction}})
125 |
126 | from kraken.lib.vgsl import TorchVGSLModel
127 | message(f'Loading ANN {model}\t', nl=False)
128 | try:
129 | model = TorchVGSLModel.load_model(model)
130 | model.to(ctx.meta['device'])
131 | except Exception:
132 | if ctx.meta['raise_failed']:
133 | raise
134 | message('\u2717', fg='red')
135 | ctx.exit(1)
136 |
137 | message('\u2713', fg='green')
138 |
139 | yolo = YOLO(yolo)
140 | yolo.to(ctx.meta["device"])
141 |
142 | return partial(segmenter, model, text_direction, mask, ctx.meta['device'], yolo, ignore_lines, deskew, max_angle)
143 |
--------------------------------------------------------------------------------
/tests/test_kraken.py:
--------------------------------------------------------------------------------
1 | import os
2 | import logging
3 | import pytest
4 | import yaml
5 | from click.testing import CliRunner
6 | from ultralytics.utils import LOGGER
7 | from yaltai.cli.yaltai import yaltai_cli
8 | from kraken.lib.xml import XMLPage
9 | from collections import defaultdict
10 | import tempfile
11 |
12 |
13 | @pytest.fixture(scope='function')
14 | def custom_logger():
15 | class CustomLoggingHandler(logging.Handler):
16 | def __init__(self):
17 | super().__init__()
18 | # A list to store log records (level and message)
19 | self.records = []
20 |
21 | def emit(self, record):
22 | # Append a tuple of the log level and the message to the records list
23 | self.records.append((record.levelname, record.getMessage()))
24 |
25 | def clear(self):
26 | self.records = []
27 |
28 | # Create a logger
29 | logger = LOGGER
30 | logger.setLevel(logging.DEBUG) # Set the logger to handle all log levels
31 |
32 | # Create and add the custom handler to the logger
33 | custom_handler = CustomLoggingHandler()
34 | logger.addHandler(custom_handler)
35 |
36 | # Clear the records list before each test
37 | custom_handler.records.clear()
38 |
39 | # Provide both the logger and handler for access during tests
40 | yield custom_handler
41 |
42 | custom_handler.records.clear()
43 |
44 | # Optional: Remove the handler after the test to prevent interference
45 | logger.removeHandler(custom_handler)
46 |
47 |
48 | def test_yaltai_single_alto_to_xml(custom_logger):
49 | """Ensures that we can convert to YOLO format"""
50 | runner = CliRunner()
51 |
52 | # Trigger a warning.
53 | result = runner.invoke(
54 | yaltai_cli,
55 | [
56 | "kraken",
57 | "--alto",
58 | "-i",
59 | os.path.join(os.path.abspath(os.path.dirname(__file__)), "test_files", "page1.jpg"),
60 | os.path.join(os.path.abspath(os.path.dirname(__file__)), "test_files", "page1.xml"),
61 | "segment",
62 | "-y",
63 | os.path.join(os.path.abspath(os.path.dirname(__file__)), "nano-yolo-ladas.pt")
64 | ]
65 | )
66 | assert result.exit_code == 0
67 | assert "page1.jpg: 640x352 2 GraphicZones, 1 MainZone-P-Continued, 1 MainZone-Sp, 2 QuireMarksZones" in "\n".join([
68 | record[1]
69 | for record in custom_logger.records
70 | ])
71 |
72 | page = XMLPage(os.path.join(os.path.abspath(os.path.dirname(__file__)), "test_files", "page1.xml"))
73 | assert {
74 | region_type: [region.boundary for region in regions]
75 | for region_type, regions in page.regions.items()
76 | } == {
77 | 'GraphicZone': [[(614.0, 12.0),
78 | (2614.0, 12.0),
79 | (2614.0, 819.0),
80 | (614.0, 819.0),
81 | (614.0, 12.0)],
82 | [(720.0, 0.0),
83 | (2634.0, 0.0),
84 | (2634.0, 343.0),
85 | (720.0, 343.0),
86 | (720.0, 0.0)]],
87 | 'MainZone-P-Continued': [[(122.0, 1536.0),
88 | (2218.0, 1536.0),
89 | (2218.0, 2888.0),
90 | (122.0, 2888.0),
91 | (122.0, 1536.0)]],
92 | 'MainZone-Sp': [[(95.0, 2974.0),
93 | (2201.0, 2974.0),
94 | (2201.0, 4854.0),
95 | (95.0, 4854.0),
96 | (95.0, 2974.0)]],
97 | 'QuireMarksZone': [[(1617.0, 4877.0),
98 | (1825.0, 4877.0),
99 | (1825.0, 4980.0),
100 | (1617.0, 4980.0),
101 | (1617.0, 4877.0)],
102 | [(1531.0, 4841.0),
103 | (1814.0, 4841.0),
104 | (1814.0, 4983.0),
105 | (1531.0, 4983.0),
106 | (1531.0, 4841.0)]]
107 | }
108 |
109 | assert len([line.baseline for line in page.lines.values()])
110 | # ToDo: Add a test to check for line being part of regions
111 |
112 |
113 | def test_alto_to_yolo_with_lines(custom_logger):
114 | """Test line region detection in ALTO to YOLO conversion"""
115 | runner = CliRunner()
116 | test_files_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), "test_files")
117 |
118 | with tempfile.TemporaryDirectory() as tempdir:
119 | result = runner.invoke(
120 | yaltai_cli,
121 | [
122 | "convert", "alto-to-yolo",
123 | os.path.join(test_files_dir, "page1.xml"),
124 | tempdir,
125 | "--line-as-region", "default"
126 | ]
127 | )
128 |
129 | assert result.exit_code == 0
130 | assert os.path.exists(f"{tempdir}/labels/page1.txt")
131 |
132 | with open(f"{tempdir}/config.yml") as f:
133 | labelmap = yaml.safe_load(f)["names"]
134 |
135 | # Verify line detection
136 | zones = defaultdict(list)
137 | with open(f"{tempdir}/labels/page1.txt") as f:
138 | for line in f:
139 | z, *position = line.split()
140 | zones[labelmap[int(z)]].append(position)
141 | assert len(zones["default"]) == 19, "There should be 19 lines found"
142 | assert zones["default"][0] == ['0.536184', '0.111331', '0.244152', '0.027338'], "First line should be this one"
143 |
--------------------------------------------------------------------------------
/yaltai/models/krakn.py:
--------------------------------------------------------------------------------
1 | from typing import Optional, Callable, Union, List, Dict, Any, Literal
2 |
3 | import PIL
4 | import logging
5 | import uuid
6 | import numpy as np
7 | import shapely.geometry as geom
8 | from kraken.blla import compute_segmentation_map, vec_lines
9 |
10 | from kraken.containers import BaselineLine, Region, Segmentation
11 | from kraken.lib.segmentation import (polygonal_reading_order, scale_regions, neural_reading_order, is_in_region)
12 | from kraken.lib import vgsl
13 | from kraken.lib.exceptions import KrakenInvalidModelException
14 | from kraken.lib.util import get_im_str
15 |
16 | logger = logging.getLogger(__name__)
17 |
18 |
19 | def region_to_objects(regions: Dict[str, List[List[int]]]) -> Dict[str, List[Region]]:
20 | new_regions = {}
21 | for region_type, list_of_regions in regions.items():
22 | new_regions[region_type] = [
23 | Region(id=str(uuid.uuid4()), boundary=x, tags={'type': region_type})
24 | for x in list_of_regions
25 | ]
26 | return new_regions
27 |
28 |
29 | def segment(im: PIL.Image.Image,
30 | text_direction: Literal['horizontal-lr', 'horizontal-rl', 'vertical-lr', 'vertical-rl'] = 'horizontal-lr',
31 | mask: Optional[np.ndarray] = None,
32 | reading_order_fn: Callable = polygonal_reading_order,
33 | model: Union[List[vgsl.TorchVGSLModel], vgsl.TorchVGSLModel] = None,
34 | device: str = 'cpu',
35 | raise_on_error: bool = False,
36 | autocast: bool = False,
37 | regions: Optional[Dict[str, List[List[int]]]] = None,
38 | ignore_lignes: bool = False) -> Segmentation:
39 | r"""
40 | Segments a page into text lines using the baseline segmenter.
41 |
42 | Segments a page into text lines and returns the polyline formed by each
43 | baseline and their estimated environment.
44 |
45 | Args:
46 | im: Input image. The mode can generally be anything but it is possible
47 | to supply a binarized-input-only model which requires accordingly
48 | treated images.
49 | text_direction: Passed-through value for serialization.serialize.
50 | mask: A bi-level mask image of the same size as `im` where 0-valued
51 | regions are ignored for segmentation purposes. Disables column
52 | detection.
53 | reading_order_fn: Function to determine the reading order. Has to
54 | accept a list of tuples (baselines, polygon) and a
55 | text direction (`lr` or `rl`).
56 | model: One or more TorchVGSLModel containing a segmentation model. If
57 | none is given a default model will be loaded.
58 | device: The target device to run the neural network on.
59 | raise_on_error: Raises error instead of logging them when they are
60 | not-blocking
61 | autocast: Runs the model with automatic mixed precision
62 |
63 | Returns:
64 | A :class:`kraken.containers.Segmentation` class containing reading
65 | order sorted baselines (polylines) and their respective polygonal
66 | boundaries as :class:`kraken.containers.BaselineLine` records. The
67 | last and first point of each boundary polygon are connected.
68 |
69 | Raises:
70 | KrakenInvalidModelException: if the given model is not a valid
71 | segmentation model.
72 | KrakenInputException: if the mask is not bitonal or does not match the
73 | image size.
74 |
75 | Notes:
76 | Multi-model operation is most useful for combining one or more region
77 | detection models and one text line model. Detected lines from all
78 | models are simply combined without any merging or duplicate detection
79 | so the chance of the same line appearing multiple times in the output
80 | are high. In addition, neural reading order determination is disabled
81 | when more than one model outputs lines.
82 | """
83 | # Unlike Kraken base implementation, we only accept Model and List of Models
84 | if isinstance(model, vgsl.TorchVGSLModel):
85 | model = [model]
86 |
87 | for nn in model:
88 | if nn.model_type != 'segmentation':
89 | raise KrakenInvalidModelException(f'Invalid model type {nn.model_type} for {nn}')
90 | if 'class_mapping' not in nn.user_metadata:
91 | raise KrakenInvalidModelException(f'Segmentation model {nn} does not contain valid class mapping')
92 |
93 | if ignore_lignes:
94 | return {'text_direction': text_direction,
95 | 'type': 'baselines',
96 | 'lines': [],
97 | 'regions': regions,
98 | 'script_detection': False}
99 |
100 | im_str = get_im_str(im)
101 | logger.info(f'Segmenting {im_str}')
102 |
103 | lines = []
104 | order = None
105 | regions = region_to_objects(regions)
106 | multi_lines = False
107 | # flag to indicate that multiple models produced line output -> disable
108 | # neural reading order
109 | for net in model:
110 | if 'topline' in net.user_metadata:
111 | loc = {None: 'center',
112 | True: 'top',
113 | False: 'bottom'}[net.user_metadata['topline']]
114 | logger.debug(f'Baseline location: {loc}')
115 |
116 | rets = compute_segmentation_map(im, mask, net, device, autocast=autocast)
117 |
118 | # We can't clear the heatmap of regions because it would mess up
119 | # print(rets)
120 | if "regions" in rets:
121 | del rets["regions"]
122 |
123 | # flatten regions for line ordering/fetch bounding regions
124 | line_regs = []
125 | suppl_obj = []
126 | for cls, regs in regions.items():
127 | line_regs.extend(regs)
128 | if rets['bounding_regions'] is not None and cls in rets['bounding_regions']:
129 | suppl_obj.extend(regs)
130 |
131 | # convert back to net scale
132 | suppl_obj = scale_regions([x.boundary for x in suppl_obj], 1/rets['scale'])
133 | line_regs = scale_regions([x.boundary for x in line_regs], 1/rets['scale'])
134 |
135 | _lines = vec_lines(**rets,
136 | regions=line_regs,
137 | text_direction=text_direction,
138 | suppl_obj=suppl_obj,
139 | topline=net.user_metadata['topline'] if 'topline' in net.user_metadata else False,
140 | raise_on_error=raise_on_error)
141 |
142 | if 'ro_model' in net.aux_layers:
143 | logger.info(f'Using reading order model found in segmentation model {net}.')
144 | _order = neural_reading_order(lines=_lines,
145 | regions=regions,
146 | text_direction=text_direction[-2:],
147 | model=net.aux_layers['ro_model'],
148 | im_size=im.size,
149 | class_mapping=net.user_metadata['ro_class_mapping'])
150 | else:
151 | _order = None
152 |
153 | if _lines and lines or multi_lines:
154 | multi_lines = True
155 | order = None
156 | logger.warning('Multiple models produced line output. This is '
157 | 'likely unintended. Suppressing neural reading '
158 | 'order.')
159 | else:
160 | order = _order
161 |
162 | lines.extend(_lines)
163 |
164 | # Rounding !
165 | for reg_class in regions:
166 | for reg_obj in regions[reg_class]:
167 | reg_obj.boundary = list(map(lambda x: list(map(round, x)), reg_obj.boundary))
168 |
169 | if len(rets['cls_map']['baselines']) > 1:
170 | script_detection = True
171 | else:
172 | script_detection = False
173 |
174 | # create objects and assign IDs
175 | blls = []
176 | _shp_regs = {}
177 | for reg_type, rgs in regions.items():
178 | for reg in rgs:
179 | _shp_regs[reg.id] = geom.Polygon(reg.boundary)
180 |
181 | # reorder lines
182 | logger.debug(f'Reordering baselines with main RO function {reading_order_fn}.')
183 | basic_lo = reading_order_fn(lines=lines, regions=_shp_regs.values(), text_direction=text_direction[-2:])
184 | lines = [lines[idx] for idx in basic_lo]
185 |
186 | for line in lines:
187 | line_regs = []
188 | for reg_id, reg in _shp_regs.items():
189 | line_ls = geom.LineString(line['baseline'])
190 | if is_in_region(line_ls, reg):
191 | line_regs.append(reg_id)
192 | blls.append(BaselineLine(id=str(uuid.uuid4()), baseline=line['baseline'], boundary=line['boundary'], tags=line['tags'], regions=line_regs))
193 |
194 | return Segmentation(text_direction=text_direction,
195 | imagename=getattr(im, 'filename', None),
196 | type='baselines',
197 | lines=blls,
198 | regions=regions,
199 | script_detection=script_detection,
200 | line_orders=[order] if order else [])
201 |
202 |
203 |
204 |
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/yaltai/cli/yaltai.py:
--------------------------------------------------------------------------------
1 | """ This CLI provides tool to transform ALTO or PAGE to YOLOv5 Formats
2 |
3 | """
4 | import glob
5 | import json
6 | import shutil
7 | import os
8 | import random
9 | import re
10 | import sys
11 | from typing import List, Optional, Union, Set, Dict
12 | from collections import Counter
13 | from pathlib import Path
14 |
15 | import numpy as np
16 | from tqdm import tqdm
17 | from PIL import Image
18 | import click
19 | import yaml
20 | import tabulate
21 |
22 |
23 | from kraken.kraken import message
24 | from kraken.lib.xml import XMLPage
25 | from yaltai.utils import AltoToYoloZone, parse_box_labels, read_labelmap, YoloV5Zone, read_manifest
26 | from mean_average_precision import MetricBuilder
27 |
28 |
29 | @click.group()
30 | def yaltai_cli():
31 | """ `yaltai` commands provides conversion options """
32 |
33 |
34 | @yaltai_cli.group("convert")
35 | def convert():
36 | """ Converts formats to various other formats """
37 |
38 |
39 | @convert.command("alto-to-yolo")
40 | @click.argument("input", type=click.Path(exists=True, dir_okay=False, file_okay=True), nargs=-1)
41 | @click.argument("output", type=click.Path(dir_okay=True, file_okay=False))
42 | @click.option("--single-class", type=str, default=None,
43 | help="Map every class to a single one")
44 | @click.option("--ignore", type=str, default=None, multiple=True)
45 | @click.option("--manifest", type=click.Path(exists=True, dir_okay=False, file_okay=True), default=None,
46 | help="Path to a manifest file containing paths to ALTO-XML files [Use with shuffle].")
47 | @click.option("--train", type=click.Path(exists=True, dir_okay=False, file_okay=True), default=None,
48 | help="Path to a manifest file containing paths to ALTO-XML files for train only [Ignores shuffle].")
49 | @click.option("--val", type=click.Path(exists=True, dir_okay=False, file_okay=True), default=None,
50 | help="Path to a manifest file containing paths to ALTO-XML files for validation only [Ignores shuffle].")
51 | @click.option("--segmonto", type=click.Choice(["region", "subtype", "full"]), default=None,
52 | help="If you use Segmonto, helper to cut the class and merge them at different levels")
53 | # ToDo: Merge classes in single class
54 | @click.option("--shuffle", type=float, default=None,
55 | help="Split into train and val")
56 | @click.option("-l", "--labelmap", type=click.Path(exists=True, file_okay=True, dir_okay=False),
57 | help="Format for the score table", default=None, show_default=True)
58 | @click.option("--image/--no-image", type=bool, default=True, show_default=True,
59 | help="Copy images when converting ALTO to YOLOv5")
60 | @click.option("--line-as-region", type=str, multiple=True,
61 | help="Line-type that should be added for zone detection")
62 | def alto_to_yolo(
63 | input: Optional[List[click.Path]],
64 | output: click.Path,
65 | single_class: Optional[str],
66 | segmonto: Optional[str],
67 | shuffle: Optional[float],
68 | labelmap: Optional[str],
69 | image: bool,
70 | manifest: Optional[click.Path],
71 | train: Optional[click.Path],
72 | val: Optional[click.Path],
73 | line_as_region: Optional[List[str]],
74 | ignore: Optional[List[str]]
75 | ):
76 |
77 | """ Converts ALTO-XML files to YOLOv5 training files
78 | """
79 | val_idx: Optional[int] = None
80 | input_paths: List[str] = []
81 |
82 | if manifest:
83 | message("Using single manifest", fg="blue")
84 | input_paths = read_manifest(manifest)
85 | elif train and val:
86 | message("Using train and validation manifests", fg="blue")
87 | train = read_manifest(train)
88 | val = read_manifest(val)
89 | val_idx = len(train)
90 | input_paths = train + val
91 | else:
92 | message(f"Using list of inputs.", fg="blue")
93 | input_paths = list(map(str, input))
94 |
95 | message(f"Found {len(input_paths)} to convert.", fg="blue")
96 |
97 | if val:
98 | message(f"{len(val)} image for validation.", fg='green')
99 | elif shuffle:
100 | random.shuffle(input_paths)
101 | val_idx = int(len(input_paths) * shuffle)
102 | message(f"{val_idx+1}/{len(input_paths)} image for validation.", fg='green')
103 |
104 | if shuffle or train:
105 | message(f"Shuffling data with a ratio of {shuffle} for validation.", fg='green')
106 | os.makedirs(f"{output}/train/labels", exist_ok=True)
107 | os.makedirs(f"{output}/val/labels", exist_ok=True)
108 | if image:
109 | os.makedirs(f"{output}/train/images", exist_ok=True)
110 | os.makedirs(f"{output}/val/images", exist_ok=True)
111 | else:
112 | os.makedirs(f"{output}/labels", exist_ok=True)
113 | if image:
114 | os.makedirs(f"{output}/images", exist_ok=True)
115 |
116 | def map_zones(zone_type: str) -> str:
117 | if segmonto:
118 | if segmonto == "full":
119 | return zone_type
120 | elif segmonto == "region":
121 | return re.search(r"([^:#]+)", zone_type).group()
122 | elif segmonto == "subtype":
123 | return re.search(r"([^#]+)", zone_type).group()
124 | elif single_class:
125 | return single_class
126 | return zone_type
127 |
128 | line_as_region: Set[str] = set(line_as_region or [])
129 |
130 | Zones: List[str] = []
131 | if labelmap:
132 | Zones = read_labelmap(labelmap)
133 |
134 | ZoneCounter = Counter()
135 |
136 | # Count Zones
137 | for idx, file in tqdm(enumerate(input_paths)):
138 | parsed = XMLPage(file)
139 | image_path: Path = parsed.imagename
140 | # We record each region identifier and map the region if required
141 | regions = parsed.regions
142 | for region in regions:
143 | if map_zones(region) not in Zones and not map_zones(region) in ignore and not region in ignore:
144 | Zones.append(map_zones(region))
145 |
146 | processed_lines: List[Dict] = []
147 |
148 | if line_as_region: # ToDo: Adapt to new system
149 | for _, line_obj in parsed.lines.items():
150 | if line_obj.tags.get("type") in line_as_region:
151 | line_type = line_obj.tags["type"]
152 | if line_type not in Zones:
153 | Zones.append(line_type)
154 | processed_lines.append(line_obj)
155 |
156 | # Retrieve image
157 | image_file = Image.open(image_path)
158 | width, height = image_file.width, image_file.height
159 | image_file.close()
160 |
161 | local_file: List[AltoToYoloZone] = []
162 | for region, examples in regions.items():
163 | mapped = map_zones(region)
164 | if region in ignore or mapped in ignore:
165 | continue
166 | region_id = Zones.index(mapped)
167 | for region_obj in examples:
168 | if region_obj.boundary:
169 | local_file.append(
170 | AltoToYoloZone(
171 | BOX=region_obj.boundary,
172 | PAGE_WIDTH=width,
173 | PAGE_HEIGHT=height,
174 | tag=region_id
175 | )
176 | )
177 | ZoneCounter[Zones[region_id]] += 1
178 |
179 | # This is only triggered if we have region_as_lines
180 | for line in processed_lines:
181 | if not line.boundary:
182 | continue
183 | region_id = Zones.index(line.tags["type"])
184 | if Zones[region_id] in ignore:
185 | continue
186 | local_file.append(
187 | AltoToYoloZone(
188 | BOX=line.boundary,
189 | PAGE_WIDTH=width,
190 | PAGE_HEIGHT=height,
191 | tag=region_id
192 | )
193 | )
194 | ZoneCounter[Zones[region_id]] += 1
195 |
196 | path = output
197 | if shuffle:
198 | path = f"{output}/train"
199 | if idx <= val_idx:
200 | path = f"{output}/val"
201 |
202 | src_img = image_path
203 | ext = src_img.suffix[1:] # Suffix keeps the dot, we remove it
204 | simplified_name = src_img.stem
205 |
206 | if image:
207 | if ext.lower() not in {"jpg", "jpeg"}:
208 | # open image in png format
209 | img_png = Image.open(src_img)
210 |
211 | if img_png.mode == "RGBA": # Handle RGBA
212 | img_png = img_png.convert('RGB')
213 |
214 | # The image object is used to save the image in jpg format
215 | img_png.save(f"{path}/images/{simplified_name}.jpg")
216 | img_png.close()
217 | else:
218 | shutil.copy(src_img, f"{path}/images/{simplified_name}.jpg")
219 |
220 | with open(f"{path}/labels/{simplified_name}.txt", "w") as f:
221 | f.write("\n".join([loc.yoloV5() for loc in local_file if loc.yoloV5()]))
222 |
223 | message(f"{len(input_paths)} ground truth XML files converted.", fg='green')
224 |
225 | for zone in ZoneCounter:
226 | if ZoneCounter[zone] == 0 and not labelmap:
227 | Zones.pop(Zones.index(zone))
228 | print(f"Zone {zone} removed from zones")
229 | for zone in ignore:
230 | if zone in Zones:
231 | Zones.pop(Zones.index(zone))
232 | print(f"Zone {zone} removed from zones")
233 |
234 | with open(f"{output}/config.yml", "w") as f:
235 | data = {
236 | "train": os.path.abspath(output),
237 | "val": os.path.abspath(output),
238 | "nc": len(Zones),
239 | "names": Zones
240 | }
241 | if shuffle:
242 | data.update({
243 | "train": f"{os.path.abspath(output)}/train/images",
244 | "val": f"{os.path.abspath(output)}/val/images"
245 | })
246 |
247 | yaml.dump(
248 | data=data,
249 | stream=f,
250 | sort_keys=False
251 | )
252 |
253 | with open(f"{output}/labelmap.txt", "w") as f:
254 | f.write("\n".join(Zones))
255 |
256 | message(f"Configuration available at {output}/config.yml.", fg='green')
257 | message(f"Label Map available at {output}/labelmap.txt.", fg='green')
258 |
259 | message(f"Regions count:", fg='blue')
260 | for zone, cnt in ZoneCounter.items():
261 | message(f"\t- {cnt:05} {zone}", fg='blue')
262 |
263 |
264 | @yaltai_cli.command("scores")
265 | @click.argument("gt-directory", type=click.Path(exists=True, dir_okay=True, file_okay=False))
266 | @click.argument("pred-directory", type=click.Path(dir_okay=True, file_okay=False, exists=True))
267 | @click.option("-t", "--threshold", type=float, help="IoU Threshold", default=.5, show_default=True)
268 | @click.option("-f", "--format", type=click.Choice(["markdown", "latex"]),
269 | help="Format for the score table", default="markdown", show_default=True)
270 | @click.option("-l", "--labelmap", type=click.Path(exists=True, file_okay=True, dir_okay=False),
271 | help="Labelmap to print nicely the information", default=None, show_default=True)
272 | @click.option("-j", "--save-json", type=click.File(mode="w"),
273 | help="JSON File to save information", default=None, show_default=True)
274 | def get_scores(gt_directory, pred_directory, threshold, format, labelmap, save_json):
275 | gt_directory = os.path.join(gt_directory, "*.txt")
276 | pred_directory = os.path.join(pred_directory, "*.txt")
277 |
278 | ground_truth, gt_arrays = parse_box_labels(sorted(glob.glob(gt_directory)))
279 | pred, pred_arrays = parse_box_labels(sorted(glob.glob(pred_directory)), gt=False)
280 |
281 | classes = np.unique(
282 | np.concatenate((
283 | np.array([row for arr in gt_arrays for row in arr])[:, 4],
284 | np.array([row for arr in pred_arrays for row in arr])[:, 4]
285 | ))
286 | ).tolist()
287 |
288 | def reclass_classes(array_list: List[np.array]) -> None:
289 | for array in array_list:
290 | for row_idx in range(array.shape[0]):
291 | array[row_idx, 4] = classes.index(array[row_idx, 4].astype(int))
292 |
293 | reclass_classes(gt_arrays)
294 | reclass_classes(pred_arrays)
295 |
296 | builder = MetricBuilder.build_evaluation_metric("map_2d", async_mode=False, num_classes=len(classes))
297 | for pred_array, gt_array in zip(pred_arrays, gt_arrays):
298 | builder.add(pred_array, gt_array)
299 |
300 | metric = builder.value(iou_thresholds=threshold)
301 | print(f"Global mAP: {metric['mAP']}")
302 |
303 | if labelmap:
304 | labelmap = read_labelmap(labelmap)
305 | else:
306 | labelmap = list(range(max(classes) + 1))
307 |
308 | table = [["Class", "AP", "Precision", "Recall", "Support"]]
309 | for cls_idx, cls_orig_idx in enumerate(classes):
310 | data = metric[0.5][cls_idx]
311 | ap, precision, recall, support = data["ap"], data["precision"].mean(), data["recall"].mean(), \
312 | data["precision"].shape[0]
313 | table.append([labelmap[cls_orig_idx], ap, precision, recall, support])
314 |
315 | print(tabulate.tabulate(table, tablefmt=format, floatfmt=".3f", headers="firstrow"))
316 |
317 | if save_json is not None:
318 | json.dump({
319 | "mAP": float(metric["mAP"]),
320 | "classes": {
321 | row[0]: {
322 | "AP": float(row[1]),
323 | "Precision": float(row[2]),
324 | "Recall": float(row[2]),
325 | "Support": float(row[3])
326 | }
327 | for row in table[1:]
328 | }
329 | }, save_json)
330 |
331 |
332 | @convert.command("yolo-to-alto")
333 | @click.argument("input", type=click.Path(exists=True, dir_okay=False, file_okay=True), nargs=-1)
334 | @click.option("-l", "--labelmap", type=click.Path(exists=True, file_okay=True, dir_okay=False),
335 | help="Labels", default=None, show_default=True)
336 | def yolo_to_alto(input, labelmap):
337 | """ Converts YOLOv5.txt files to ALTO files """
338 | if not labelmap:
339 | message("No labelmap given, --labelmap is required for ALTO conversion", fg="red")
340 | sys.exit(0)
341 |
342 | labelmap = read_labelmap(labelmap)
343 |
344 | OtherTags = "\n".join([
345 | f''
346 | for idx, zone in enumerate(labelmap)
347 | ])
348 |
349 | with open(os.path.join(os.path.dirname(__file__), "../template.xml")) as f:
350 | TEMPLATE = f.read()
351 |
352 | for file in input:
353 | xml_name = file[:-4] + ".xml"
354 | img_file_name = os.path.basename(file[:-4]) + ".jpg"
355 | zones = []
356 | if os.path.exists(os.path.join(os.path.dirname(file), "..", "images", img_file_name)):
357 | img_name = os.path.join(os.path.dirname(file), "..", "images", img_file_name)
358 | img_for_xml_name = f"../images/{img_file_name}"
359 | elif os.path.exists(os.path.join(os.path.dirname(file), "../..", "images", img_file_name)):
360 | img_name = os.path.join(os.path.dirname(file), "../..", "images", img_file_name)
361 | img_for_xml_name = os.path.join("../..", img_file_name)
362 | else:
363 | message(f"Can't find the image for {img_file_name}")
364 | sys.exit(0)
365 |
366 | image = Image.open(img_name)
367 | img_width, img_height = image.size
368 | image.close()
369 |
370 | with open(file) as f:
371 | for line_idx, line in enumerate(f):
372 | z = YoloV5Zone.from_txt(*line.strip().split()[:5])
373 |
374 | x0, y0, x1, y1 = z.xyxy
375 | x0, x1 = img_width*x0, img_width*x1
376 | y0, y1 = img_height*y0, img_height*y1
377 | x0, x1, y0, y1 = [int(z) for z in [x0, x1, y0, y1]]
378 | width = x1 - x0
379 | height = y1 - y0
380 |
381 | zones.append(f"""
382 |
386 |
387 |
388 |
389 | """)
390 |
391 | with open(xml_name, "w") as f:
392 | f.write(
393 | TEMPLATE.replace("%Filename%", img_for_xml_name)
394 | .replace("%Width%", str(img_width))
395 | .replace("%Height%", str(img_height))
396 | .replace("%Tags%", OtherTags)
397 | .replace("%Textblocks%", "".join(zones))
398 | )
399 |
400 |
401 | from yaltai.cli.krakn import kcli
402 |
403 | yaltai_cli.add_command(kcli, "kraken")
404 |
405 |
406 | if __name__ == "__main__":
407 | yaltai_cli()
408 |
--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
1 | GNU GENERAL PUBLIC LICENSE
2 | Version 3, 29 June 2007
3 |
4 | Copyright (C) 2007 Free Software Foundation, Inc.
5 | Everyone is permitted to copy and distribute verbatim copies
6 | of this license document, but changing it is not allowed.
7 |
8 | Preamble
9 |
10 | The GNU General Public License is a free, copyleft license for
11 | software and other kinds of works.
12 |
13 | The licenses for most software and other practical works are designed
14 | to take away your freedom to share and change the works. By contrast,
15 | the GNU General Public License is intended to guarantee your freedom to
16 | share and change all versions of a program--to make sure it remains free
17 | software for all its users. We, the Free Software Foundation, use the
18 | GNU General Public License for most of our software; it applies also to
19 | any other work released this way by its authors. You can apply it to
20 | your programs, too.
21 |
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343 | 7. Additional Terms.
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435 | 9. Acceptance Not Required for Having Copies.
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471 | 11. Patents.
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473 | A "contributor" is a copyright holder who authorizes use under this
474 | License of the Program or a work on which the Program is based. The
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477 | A contributor's "essential patent claims" are all patent claims
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535 |
536 | Nothing in this License shall be construed as excluding or limiting
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539 |
540 | 12. No Surrender of Others' Freedom.
541 |
542 | If conditions are imposed on you (whether by court order, agreement or
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548 | to collect a royalty for further conveying from those to whom you convey
549 | the Program, the only way you could satisfy both those terms and this
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551 |
552 | 13. Use with the GNU Affero General Public License.
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554 | Notwithstanding any other provision of this License, you have
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560 | section 13, concerning interaction through a network will apply to the
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562 |
563 | 14. Revised Versions of this License.
564 |
565 | The Free Software Foundation may publish revised and/or new versions of
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567 | be similar in spirit to the present version, but may differ in detail to
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569 |
570 | Each version is given a distinguishing version number. If the
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573 | option of following the terms and conditions either of that numbered
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578 |
579 | If the Program specifies that a proxy can decide which future
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587 | later version.
588 |
589 | 15. Disclaimer of Warranty.
590 |
591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
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599 |
600 | 16. Limitation of Liability.
601 |
602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
610 | SUCH DAMAGES.
611 |
612 | 17. Interpretation of Sections 15 and 16.
613 |
614 | If the disclaimer of warranty and limitation of liability provided
615 | above cannot be given local legal effect according to their terms,
616 | reviewing courts shall apply local law that most closely approximates
617 | an absolute waiver of all civil liability in connection with the
618 | Program, unless a warranty or assumption of liability accompanies a
619 | copy of the Program in return for a fee.
620 |
621 | END OF TERMS AND CONDITIONS
622 |
623 | How to Apply These Terms to Your New Programs
624 |
625 | If you develop a new program, and you want it to be of the greatest
626 | possible use to the public, the best way to achieve this is to make it
627 | free software which everyone can redistribute and change under these terms.
628 |
629 | To do so, attach the following notices to the program. It is safest
630 | to attach them to the start of each source file to most effectively
631 | state the exclusion of warranty; and each file should have at least
632 | the "copyright" line and a pointer to where the full notice is found.
633 |
634 |
635 | Copyright (C)
636 |
637 | This program is free software: you can redistribute it and/or modify
638 | it under the terms of the GNU General Public License as published by
639 | the Free Software Foundation, either version 3 of the License, or
640 | (at your option) any later version.
641 |
642 | This program is distributed in the hope that it will be useful,
643 | but WITHOUT ANY WARRANTY; without even the implied warranty of
644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
645 | GNU General Public License for more details.
646 |
647 | You should have received a copy of the GNU General Public License
648 | along with this program. If not, see .
649 |
650 | Also add information on how to contact you by electronic and paper mail.
651 |
652 | If the program does terminal interaction, make it output a short
653 | notice like this when it starts in an interactive mode:
654 |
655 | Copyright (C)
656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
657 | This is free software, and you are welcome to redistribute it
658 | under certain conditions; type `show c' for details.
659 |
660 | The hypothetical commands `show w' and `show c' should show the appropriate
661 | parts of the General Public License. Of course, your program's commands
662 | might be different; for a GUI interface, you would use an "about box".
663 |
664 | You should also get your employer (if you work as a programmer) or school,
665 | if any, to sign a "copyright disclaimer" for the program, if necessary.
666 | For more information on this, and how to apply and follow the GNU GPL, see
667 | .
668 |
669 | The GNU General Public License does not permit incorporating your program
670 | into proprietary programs. If your program is a subroutine library, you
671 | may consider it more useful to permit linking proprietary applications with
672 | the library. If this is what you want to do, use the GNU Lesser General
673 | Public License instead of this License. But first, please read
674 | .
675 |
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